pyhml package¶
pyhml¶
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class
pyhml.pyhml.
HmlParser
(hmlversion: str = None, verbose: bool = False)[source]¶ Bases:
object
A python HML parser that converts any valid HML file into an python
object
. Allows users to easily interact with HML data as python objects. Users can also easily convert the HML data to a pandas DataFrame. If nohmlversion
is provided, then the schemas for all HML versions are loaded.Examples:
>>> import pyhml >>> hmlparser = pyhml.HmlParser(verbose=True) >>> hml = hmlparser.parse(hml_file) >>> hml_df = hml.toPandas()
Parameters: - hmlversion (str) – A specific HML version to load.
- verbose (bool) – Flag for running in verbose.
Data Objects¶
HML¶
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class
pyhml.models.hml.
HML
(project_name: str = None, version: str = None, schema_location: str = None, reporting_center: pyhml.models.reporting_center.ReportingCenter = None, sample: List[pyhml.models.sample.Sample] = None)[source]¶ Bases:
pyhml.models.base_model_.Model
NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.
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classmethod
from_dict
(dikt) → pyhml.models.hml.HML[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The HML of this HML. Return type: HML
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project_name
¶ Gets the project_name of this HML.
Returns: The project_name of this HML. Return type: str
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reporting_center
¶ Gets the reporting_center of this HML.
Returns: The reporting_center of this HML. Return type: ReportingCenter
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schema_location
¶ Gets the schema_location of this HML.
Returns: The schema_location of this HML. Return type: str
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toPandas
() → pandas.core.frame.DataFrame[source]¶ Returns all the HML data as a pandas DataFrame.
Examples:
>>> import pyhml >>> hmlparser = pyhml.HmlParser(verbose=True) >>> hml = hmlparser.parse(hml_file) >>> hml_df = hml.toPandas()
Returns: Pandas dataframe Return type: DataFrame
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tobiotype
(outdir, dtype='fasta', by='file')[source]¶ Converts an HML object to a BioPython data fromat
Examples:
>>> import pyhml >>> hmlparser = pyhml.HmlParser(verbose=True) >>> hml = hmlparser.parse(hml_file) >>> hml.tobiotype("output/directory",dtype='imgt', by='subject')
Parameters: - outdir (str) – The output directory
- dtype – The BioPython output type
- by (str) – What to print out the HML file by
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version
¶ Gets the version of this HML.
Returns: The version of this HML. Return type: str
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classmethod
Sample¶
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class
pyhml.models.sample.
Sample
(center_code: int = None, id: str = None, collection_method: str = None, typing: List[pyhml.models.typing.Typing] = None)[source]¶ Bases:
pyhml.models.base_model_.Model
Examples:
>>> from pyhml.models.typing import Typing >>> from pyhml.models.sample import Sample
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center_code
¶ Gets the center_code of this Sample.
Returns: The center_code of this Sample. Return type: int
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collection_method
¶ Gets the collection_method of this Sample.
Returns: The collection_method of this Sample. Return type: str
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classmethod
from_dict
(dikt) → pyhml.models.sample.Sample[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The Sample of this Sample. Return type: Sample
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id
¶ Gets the id of this Sample.
Returns: The id of this Sample. Return type: str
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seq_records
¶ Gets the seq_records of this Sample.
Returns: The seq_records of this Sample. Return type: Dict
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Typing¶
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class
pyhml.models.typing.
Typing
(date: str = None, gene_family: str = None, allele_assignment: List[pyhml.models.allele_assignment.AlleleAssignment] = None, consensus_sequence: List[pyhml.models.consensus.Consensus] = None, typing_method: pyhml.models.typing_method.TypingMethod = None)[source]¶ Bases:
pyhml.models.base_model_.Model
NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.
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allele_assignment
¶ Gets the allele_assignment of this Typing.
Returns: The allele_assignment of this Typing. Return type: List[AlleleAssignment]
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consensus_sequence
¶ Gets the consensus_sequence of this Typing.
Returns: The consensus_sequence of this Typing. Return type: List[Consensus]
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date
¶ Gets the date of this Typing.
Returns: The date of this Typing. Return type: str
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classmethod
from_dict
(dikt) → pyhml.models.typing.Typing[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The Typing of this Typing. Return type: Typing
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gene_family
¶ Gets the gene_family of this Typing.
Returns: The gene_family of this Typing. Return type: str
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seq_records
¶ Gets the seq_records of this ReferenceData.
Returns: The seq_records of this ReferenceData. Return type: List[SeqRecord]
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typing_method
¶ Gets the typing_method of this Typing.
Returns: The typing_method of this Typing. Return type: TypingMethod
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Consensus¶
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class
pyhml.models.consensus.
Consensus
(date: str = None, consensus_sequence_block: List[pyhml.models.consensus_seq_block.ConsensusSeqBlock] = None, reference_database: List[pyhml.models.ref_database.RefDatabase] = None)[source]¶ Bases:
pyhml.models.base_model_.Model
NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.
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consensus_sequence_block
¶ Gets the consensus_sequence_block of this Consensus.
Returns: The consensus_sequence_block of this Consensus. Return type: List[ConsensusSeqBlock]
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date
¶ Gets the date of this Consensus.
Returns: The date of this Consensus. Return type: str
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classmethod
from_dict
(dikt) → pyhml.models.consensus.Consensus[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The Consensus of this Consensus. Return type: Consensus
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reference_database
¶ Gets the reference_database of this Consensus.
Returns: The reference_database of this Consensus. Return type: List[RefDatabase]
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Consensus Block¶
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class
pyhml.models.consensus_seq_block.
ConsensusSeqBlock
(continuity: bool = None, description: str = None, end: int = None, expected_copy_number: int = None, phase_set: str = None, reference_sequence_id: str = None, start: int = None, strand: str = None, sequence: Bio.Seq.Seq = None, sequence_quality: List[pyhml.models.seq_quality.SeqQuality] = None, variant: List[pyhml.models.variant.Variant] = None)[source]¶ Bases:
pyhml.models.base_model_.Model
NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.
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continuity
¶ Gets the continuity of this ConsensusSeqBlock.
Returns: The continuity of this ConsensusSeqBlock. Return type: bool
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description
¶ Gets the description of this ConsensusSeqBlock.
Returns: The description of this ConsensusSeqBlock. Return type: str
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end
¶ Gets the end of this ConsensusSeqBlock.
Returns: The end of this ConsensusSeqBlock. Return type: int
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expected_copy_number
¶ Gets the expected_copy_number of this ConsensusSeqBlock.
Returns: The expected_copy_number of this ConsensusSeqBlock. Return type: int
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classmethod
from_dict
(dikt) → pyhml.models.consensus_seq_block.ConsensusSeqBlock[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The ConsensusSeqBlock of this ConsensusSeqBlock. Return type: ConsensusSeqBlock
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phase_set
¶ Gets the phase_set of this ConsensusSeqBlock.
Returns: The phase_set of this ConsensusSeqBlock. Return type: str
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reference_sequence_id
¶ Gets the reference_sequence_id of this ConsensusSeqBlock.
Returns: The reference_sequence_id of this ConsensusSeqBlock. Return type: str
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sequence
¶ Gets the sequence of this ConsensusSeqBlock.
Returns: The sequence of this ConsensusSeqBlock. Return type: Seq
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sequence_quality
¶ Gets the sequence_quality of this ConsensusSeqBlock.
Returns: The sequence_quality of this ConsensusSeqBlock. Return type: List[SeqQuality]
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start
¶ Gets the start of this ConsensusSeqBlock.
Returns: The start of this ConsensusSeqBlock. Return type: int
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strand
¶ Gets the strand of this ConsensusSeqBlock.
Returns: The strand of this ConsensusSeqBlock. Return type: str
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variant
¶ Gets the variant of this ConsensusSeqBlock.
Returns: The variant of this ConsensusSeqBlock. Return type: List[Variant]
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Allele Assignment¶
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class
pyhml.models.allele_assignment.
AlleleAssignment
(allele_db: str = None, allele_version: str = None, date: str = None, glstring: List[str] = None, haploid: List[pyhml.models.haploid.Haploid] = None)[source]¶ Bases:
pyhml.models.base_model_.Model
NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.
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allele_db
¶ Gets the allele_db of this AlleleAssignment.
Returns: The allele_db of this AlleleAssignment. Return type: str
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allele_version
¶ Gets the allele_version of this AlleleAssignment.
Returns: The allele_version of this AlleleAssignment. Return type: str
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date
¶ Gets the date of this AlleleAssignment.
Returns: The date of this AlleleAssignment. Return type: str
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classmethod
from_dict
(dikt) → pyhml.models.allele_assignment.AlleleAssignment[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The AlleleAssignment of this AlleleAssignment. Return type: AlleleAssignment
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glstring
¶ Gets the glstring of this AlleleAssignment.
Returns: The glstring of this AlleleAssignment. Return type: List[str]
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haploid
¶ Gets the haploid of this AlleleAssignment.
Returns: The haploid of this AlleleAssignment. Return type: List[Haploid]
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Allele Assignment¶
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class
pyhml.models.allele_assignment.
AlleleAssignment
(allele_db: str = None, allele_version: str = None, date: str = None, glstring: List[str] = None, haploid: List[pyhml.models.haploid.Haploid] = None)[source] Bases:
pyhml.models.base_model_.Model
NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.
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allele_db
Gets the allele_db of this AlleleAssignment.
Returns: The allele_db of this AlleleAssignment. Return type: str
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allele_version
Gets the allele_version of this AlleleAssignment.
Returns: The allele_version of this AlleleAssignment. Return type: str
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date
Gets the date of this AlleleAssignment.
Returns: The date of this AlleleAssignment. Return type: str
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classmethod
from_dict
(dikt) → pyhml.models.allele_assignment.AlleleAssignment[source] Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The AlleleAssignment of this AlleleAssignment. Return type: AlleleAssignment
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glstring
Gets the glstring of this AlleleAssignment.
Returns: The glstring of this AlleleAssignment. Return type: List[str]
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haploid
Gets the haploid of this AlleleAssignment.
Returns: The haploid of this AlleleAssignment. Return type: List[Haploid]
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